rs11157219

chr14-41313498-A-Gchr14-41313498-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.234 in 152,132 control chromosomes in the GnomAD database, including 4,436 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35645 AN: 152014 Hom.: 4435 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.234 AC: 35644 AN: 152132 Hom.: 4436 Cov.: 32 AF XY: 0.233 AC XY: 17363 AN XY: 74366

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.220

Alfa AF: 0.260 Hom.: 8885

Bravo AF: 0.225

Asia WGS AF: 0.236 AC: 820 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
Cadd	Benign	18
Dann	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11157219; hg19: chr14-41782701;